Dear all,
I want to use cPlot and cColor from the geneplotter package to
visualise the intensity level of some genes from a microarray
experiment on their given chromosomal location. However, I'm slightly
confused by the results, especially since the colours don't really
match what I get using alongChrom().
An example is shown below, using Entrez IDs. In this case I would
expect the first probe in the "probes" argument to be associated with
the first colour in "color" and so on, but that doesn't seem to be
the case. At least not for my versions of the packages.
Any comments would be appreciated. Also, out of curiosity, what
happens with those IDs that map to several locations within the
genome, such as no. 19 and 64 in my xx list. Will the "color"
argument automatically take that into consideration?
Thanks
\Heidi
library(geneplotter)
library(org.Mm.eg.db)
library(RColorBrewer)
# Test
x <- org.Mm.egCHRLOC
mapped_genes <- mappedkeys(x)
xx <- as.list(x[mapped_genes])
chr <- buildChromLocation("org.Mm.eg.db")
cPlot(chr)
cColor(probes=names(xx[1:4]), color=c("red", "green", "blue",
"purple"), plotChroms=chr)
# A (simplified) example similar to the vignette
dec <- quantile(0:100, probs=seq(0,1,0.1))
class <- cut(1:100, dec)
col <- brewer.pal(10, "RdYlGn")
cPlot(chr)
cColor(probes=names(xx[1:100]), color=col[class], plotChroms=chr)
sessionInfo()
R version 2.7.0 Patched (2008-05-18 r45723)
i386-apple-darwin8.10.1
locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] tools stats graphics grDevices utils datasets
methods base
other attached packages:
[1] RColorBrewer_1.0-2 org.Mm.eg.db_2.2.0 geneplotter_1.18.0
annotate_1.18.0 xtable_1.5-2
[6] AnnotationDbi_1.2.0 RSQLite_0.6-8 DBI_0.2-4
lattice_0.17-7 Biobase_2.0.1
loaded via a namespace (and not attached):
[1] KernSmooth_2.22-22 grid_2.7.0